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Maraslioglu-Sperber A, Pizzi E, Fisch JO, Kattler K, Ritter T, Friauf E. Molecular and functional profiling of cell diversity and identity in the lateral superior olive, an auditory brainstem center with ascending and descending projections. Front Cell Neurosci 2024; 18:1354520. [PMID: 38846638 PMCID: PMC11153811 DOI: 10.3389/fncel.2024.1354520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/15/2024] [Indexed: 06/09/2024] Open
Abstract
The lateral superior olive (LSO), a prominent integration center in the auditory brainstem, contains a remarkably heterogeneous population of neurons. Ascending neurons, predominantly principal neurons (pLSOs), process interaural level differences for sound localization. Descending neurons (lateral olivocochlear neurons, LOCs) provide feedback into the cochlea and are thought to protect against acoustic overload. The molecular determinants of the neuronal diversity in the LSO are largely unknown. Here, we used patch-seq analysis in mice at postnatal days P10-12 to classify developing LSO neurons according to their functional and molecular profiles. Across the entire sample (n = 86 neurons), genes involved in ATP synthesis were particularly highly expressed, confirming the energy expenditure of auditory neurons. Two clusters were identified, pLSOs and LOCs. They were distinguished by 353 differentially expressed genes (DEGs), most of which were novel for the LSO. Electrophysiological analysis confirmed the transcriptomic clustering. We focused on genes affecting neuronal input-output properties and validated some of them by immunohistochemistry, electrophysiology, and pharmacology. These genes encode proteins such as osteopontin, Kv11.3, and Kvβ3 (pLSO-specific), calcitonin-gene-related peptide (LOC-specific), or Kv7.2 and Kv7.3 (no DEGs). We identified 12 "Super DEGs" and 12 genes showing "Cluster similarity." Collectively, we provide fundamental and comprehensive insights into the molecular composition of individual ascending and descending neurons in the juvenile auditory brainstem and how this may relate to their specific functions, including developmental aspects.
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Affiliation(s)
- Ayse Maraslioglu-Sperber
- Animal Physiology Group, Department of Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Erika Pizzi
- Animal Physiology Group, Department of Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Jonas O. Fisch
- Animal Physiology Group, Department of Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Kathrin Kattler
- Genetics/Epigenetics Group, Department of Biological Sciences, Saarland University, Saarbrücken, Germany
| | - Tamara Ritter
- Animal Physiology Group, Department of Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Eckhard Friauf
- Animal Physiology Group, Department of Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
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2
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Kim YJ, Jeong IH, Ha JH, Kim YS, Sung S, Jang JH, Choung YH. The Suppression of Ubiquitin C-Terminal Hydrolase L1 Promotes the Transdifferentiation of Auditory Supporting Cells into Hair Cells by Regulating the mTOR Pathway. Cells 2024; 13:737. [PMID: 38727276 PMCID: PMC11083094 DOI: 10.3390/cells13090737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
In mammals, hearing loss is irreversible due to the lack of the regenerative capacity of the auditory epithelium. However, stem/progenitor cells in mammalian cochleae may be a therapeutic target for hearing regeneration. The ubiquitin proteasome system plays an important role in cochlear development and maintenance. In this study, we investigated the role of ubiquitin C-terminal hydrolase L1 (UCHL1) in the process of the transdifferentiation of auditory supporting cells (SCs) into hair cells (HCs). The expression of UCHL1 gradually decreased as HCs developed and was restricted to inner pillar cells and third-row Deiters' cells between P2 and P7, suggesting that UCHL1-expressing cells are similar to the cells with Lgr5-positive progenitors. UCHL1 expression was decreased even under conditions in which supernumerary HCs were generated with a γ-secretase inhibitor and Wnt agonist. Moreover, the inhibition of UCHL1 by LDN-57444 led to an increase in HC numbers. Mechanistically, LDN-57444 increased mTOR complex 1 activity and allowed SCs to transdifferentiate into HCs. The suppression of UCHL1 induces the transdifferentiation of auditory SCs and progenitors into HCs by regulating the mTOR pathway.
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Affiliation(s)
- Yeon Ju Kim
- Department of Otolaryngology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (Y.J.K.); (J.H.H.); (Y.S.K.); (J.H.J.)
| | - In Hye Jeong
- Department of Medical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea; (I.H.J.); (S.S.)
| | - Jung Ho Ha
- Department of Otolaryngology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (Y.J.K.); (J.H.H.); (Y.S.K.); (J.H.J.)
- Department of Medical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea; (I.H.J.); (S.S.)
| | - Young Sun Kim
- Department of Otolaryngology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (Y.J.K.); (J.H.H.); (Y.S.K.); (J.H.J.)
| | - Siung Sung
- Department of Medical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea; (I.H.J.); (S.S.)
| | - Jeong Hun Jang
- Department of Otolaryngology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (Y.J.K.); (J.H.H.); (Y.S.K.); (J.H.J.)
| | - Yun-Hoon Choung
- Department of Otolaryngology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (Y.J.K.); (J.H.H.); (Y.S.K.); (J.H.J.)
- Department of Medical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea; (I.H.J.); (S.S.)
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3
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Cepeda AP, Ninov M, Neef J, Parfentev I, Kusch K, Reisinger E, Jahn R, Moser T, Urlaub H. Proteomic Analysis Reveals the Composition of Glutamatergic Organelles of Auditory Inner Hair Cells. Mol Cell Proteomics 2024; 23:100704. [PMID: 38128648 PMCID: PMC10832297 DOI: 10.1016/j.mcpro.2023.100704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/08/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Abstract
In the ear, inner hair cells (IHCs) employ sophisticated glutamatergic ribbon synapses with afferent neurons to transmit auditory information to the brain. The presynaptic machinery responsible for neurotransmitter release in IHC synapses includes proteins such as the multi-C2-domain protein otoferlin and the vesicular glutamate transporter 3 (VGluT3). Yet, much of this likely unique molecular machinery remains to be deciphered. The scarcity of material has so far hampered biochemical studies which require large amounts of purified samples. We developed a subcellular fractionation workflow combined with immunoisolation of VGluT3-containing membrane vesicles, allowing for the enrichment of glutamatergic organelles that are likely dominated by synaptic vesicles (SVs) of IHCs. We have characterized their protein composition in mice before and after hearing onset using mass spectrometry and confocal imaging and provide a fully annotated proteome with hitherto unidentified proteins. Despite the prevalence of IHC marker proteins across IHC maturation, the profiles of trafficking proteins differed markedly before and after hearing onset. Among the proteins enriched after hearing onset were VAMP-7, syntaxin-7, syntaxin-8, syntaxin-12/13, SCAMP1, V-ATPase, SV2, and PKCα. Our study provides an inventory of the machinery associated with synaptic vesicle-mediated trafficking and presynaptic activity at IHC ribbon synapses and serves as a foundation for future functional studies.
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Affiliation(s)
- Andreia P Cepeda
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Momchil Ninov
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Jakob Neef
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany; Auditory Neuroscience & Synaptic Nanophysiology Group Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Iwan Parfentev
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Kathrin Kusch
- Functional Auditory Genomics Group, Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Ellen Reisinger
- Gene Therapy for Hearing Impairment and Deafness, Department for Otolaryngology, Head & Neck Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Reinhard Jahn
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - Tobias Moser
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany; Auditory Neuroscience & Synaptic Nanophysiology Group Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
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4
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Sun P, Smith E, Nicolson T. Transmembrane Channel-Like (Tmc) Subunits Contribute to Frequency Sensitivity in the Zebrafish Utricle. J Neurosci 2024; 44:e1298232023. [PMID: 37952940 PMCID: PMC10851681 DOI: 10.1523/jneurosci.1298-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/25/2023] [Accepted: 09/16/2023] [Indexed: 11/14/2023] Open
Abstract
Information about dynamic head motion is conveyed by a central "striolar" zone of vestibular hair cells and afferent neurons in the inner ear. How vestibular hair cells are tuned to transduce dynamic stimuli at the molecular level is not well understood. Here we take advantage of the differential expression pattern of tmc1, tmc2a, and tmc2b, which encode channel subunits of the mechanotransduction complex in zebrafish vestibular hair cells. To test the role of various combinations of Tmc subunits in transducing dynamic head movements, we measured reflexive eye movements induced by high-frequency stimuli in single versus double tmc mutants. We found that Tmc2a function correlates with the broadest range of frequency sensitivity, whereas Tmc2b mainly contributes to lower-frequency responses. Tmc1, which is largely excluded from the striolar zone, plays a minor role in sensing lower-frequency stimuli. Our study suggests that the Tmc subunits impart functional differences to the mechanotransduction of dynamic stimuli.Significance Statement Information about dynamic head movements is transmitted by sensory receptors, known as hair cells, in the labyrinth of the inner ear. The sensitivity of hair cells to fast or slow movements of the head differs according to cell type. Whether the mechanotransduction complex that converts mechanical stimuli into electrical signals in hair cells participates in conveying frequency information is not clear. Here we find that the transmembrane channel-like 1/2 genes, which encode a central component of the complex, are differentially expressed in the utricle and contribute to frequency sensitivity in zebrafish.
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Affiliation(s)
- Peng Sun
- Department of Otolaryngology, Stanford University, Stanford, California 94304
| | - Eliot Smith
- Department of Otolaryngology, Stanford University, Stanford, California 94304
| | - Teresa Nicolson
- Department of Otolaryngology, Stanford University, Stanford, California 94304
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5
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Hertzano R, Gwilliam K, Rose K, Milon B, Matern MS. Cell Type-Specific Expression Analysis of the Inner Ear: A Technical Report. Laryngoscope 2021; 131 Suppl 5:S1-S16. [PMID: 32579737 PMCID: PMC8996438 DOI: 10.1002/lary.28765] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/21/2020] [Accepted: 05/01/2020] [Indexed: 01/11/2023]
Abstract
OBJECTIVE The cellular diversity of the inner ear has presented a technical challenge in obtaining molecular insight into its development and function. The application of technological advancements in cell type-specific expression enable clinicians and researchers to leap forward from classic genetics to obtaining mechanistic understanding of congenital and acquired hearing loss. This understanding is essential for development of therapeutics to prevent and reverse diseases of the inner ear, including hearing loss. The objective of this study is to describe and compare the available tools for cell type-specific analysis of the ear, as a means to support decision making in study design. STUDY DESIGN Three major approaches for cell type-specific analysis of the ear including fluorescence-activated cell sorting (FACS), ribosomal and RNA pulldown techniques, and single cell RNA-seq (scRNA-seq) are compared and contrasted using both published and original data. RESULTS We demonstrate the strength and weaknesses of these approaches leading to the inevitable conclusion that to maximize the utility of these approaches, it is important to match the experimental approach with the tissue of origin, cell type of interest, and the biological question. Often, a combined approach (eg, cell sorting and scRNA-seq or expression analysis using 2 separate approaches) is required. Finally, new tools for visualization and analysis of complex expression data, such as the gEAR platform (umgear.org), collate cell type-specific gene expression from the ear field and provide unprecedented access to both clinicians and researchers. LEVEL OF EVIDENCE N/A Laryngoscope, 131:S1-S16, 2021.
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Affiliation(s)
- Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore Maryland U.S.A
- Department of Anatomy and Neurobiology University of Maryland School of Medicine Baltimore Maryland U.S.A
| | - Kathleen Gwilliam
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
| | - Kevin Rose
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
| | - Beatrice Milon
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
| | - Maggie S. Matern
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
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6
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Zhu Y, Scheibinger M, Ellwanger DC, Krey JF, Choi D, Kelly RT, Heller S, Barr-Gillespie PG. Single-cell proteomics reveals changes in expression during hair-cell development. eLife 2019; 8:50777. [PMID: 31682227 PMCID: PMC6855842 DOI: 10.7554/elife.50777] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/01/2019] [Indexed: 12/12/2022] Open
Abstract
Hearing and balance rely on small sensory hair cells that reside in the inner ear. To explore dynamic changes in the abundant proteins present in differentiating hair cells, we used nanoliter-scale shotgun mass spectrometry of single cells, each ~1 picoliter, from utricles of embryonic day 15 chickens. We identified unique constellations of proteins or protein groups from presumptive hair cells and from progenitor cells. The single-cell proteomes enabled the de novo reconstruction of a developmental trajectory using protein expression levels, revealing proteins that greatly increased in expression during differentiation of hair cells (e.g., OCM, CRABP1, GPX2, AK1, GSTO1) and those that decreased during differentiation (e.g., TMSB4X, AGR3). Complementary single-cell transcriptome profiling showed corresponding changes in mRNA during maturation of hair cells. Single-cell proteomics data thus can be mined to reveal features of cellular development that may be missed with transcriptomics.
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Affiliation(s)
- Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, United States
| | - Mirko Scheibinger
- Department of Otolaryngology Head and Neck Surgery, Stanford University, Stanford, United States
| | - Daniel Christian Ellwanger
- Department of Otolaryngology Head and Neck Surgery, Stanford University, Stanford, United States.,Genome Analysis Unit, Amgen Research, Amgen Inc, South San Francisco, United States
| | - Jocelyn F Krey
- Oregon Hearing Research Center, Oregon Health & Science University, Portland, United States.,Vollum Institute, Oregon Health & Science University, Portland, United States
| | - Dongseok Choi
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, United States.,Graduate School of Dentistry, Kyung Hee University, Seoul, Republic of Korea
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, United States.,Department of Chemistry and Biochemistry, Brigham Young University, Provo, United States
| | - Stefan Heller
- Department of Otolaryngology Head and Neck Surgery, Stanford University, Stanford, United States
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center, Oregon Health & Science University, Portland, United States.,Vollum Institute, Oregon Health & Science University, Portland, United States
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7
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Kim YJ, Kim K, Lee YY, Choo OS, Jang JH, Choung YH. Downregulated UCHL1 Accelerates Gentamicin-Induced Auditory Cell Death via Autophagy. Mol Neurobiol 2019; 56:7433-7447. [PMID: 31041655 DOI: 10.1007/s12035-019-1598-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 04/02/2019] [Indexed: 01/02/2023]
Abstract
The clinical use of aminoglycoside antibiotics is partly limited by their ototoxicity. The pathogenesis of aminoglycoside-induced ototoxicity still remains unknown. Here, RNA-sequencing was conducted to identify differentially expressed genes in rat cochlear organotypic cultures treated with gentamicin (GM), and 232 and 43 genes were commonly up- and downregulated, respectively, at day 1 and 2 after exposure. Ubiquitin carboxyl-terminal hydrolase isozyme L1 (Uchl1) was one of the downregulated genes whose expression was prominent in spiral ganglion cells (SGCs), lateral walls, as well as efferent nerve terminal and nerve fibers. We further investigated if a deficit of Uchl1 in organotypic cochlea and the House Ear Institute-Organ of Corti 1 (HEI-OC1) cells accelerates ototoxicity. We found that a deficit in Uchl1 accelerated GM-induced ototoxicity by showing a decreased number of SGCs and nerve fibers in organotypic cochlear cultures and HEI-OC1 cells. Furthermore, Uchl1-depleted HEI-OC1 cells revealed an increased number of autophagosomes accompanied by decreased lysosomal fusion. These data indicate that the downregulation of Uchl1 following GM treatment is deleterious to auditory cell survival, which results from the impaired autophagic flux. Our results provide evidence that UCHL1-dependent autophagic flux may have a potential as an otoprotective target for the treatment of GM-induced auditory cell death.
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Affiliation(s)
- Yeon Ju Kim
- Department of Otolaryngology, Ajou University School of Medicine, San 5 Woncheon-dong, Yeongtong-gu, Suwon, 443-721, Republic of Korea
| | - Kyung Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yun Yeong Lee
- Department of Otolaryngology, Ajou University School of Medicine, San 5 Woncheon-dong, Yeongtong-gu, Suwon, 443-721, Republic of Korea
| | - Oak-Sung Choo
- Department of Otolaryngology, Ajou University School of Medicine, San 5 Woncheon-dong, Yeongtong-gu, Suwon, 443-721, Republic of Korea.,Department of Medical Sciences, Ajou University Graduate School of Medicine, San 5 Woncheon-dong, Yeongtong-gu, Suwon, 443-721, Republic of Korea
| | - Jeong Hun Jang
- Department of Otolaryngology, Ajou University School of Medicine, San 5 Woncheon-dong, Yeongtong-gu, Suwon, 443-721, Republic of Korea
| | - Yun-Hoon Choung
- Department of Otolaryngology, Ajou University School of Medicine, San 5 Woncheon-dong, Yeongtong-gu, Suwon, 443-721, Republic of Korea. .,Department of Medical Sciences, Ajou University Graduate School of Medicine, San 5 Woncheon-dong, Yeongtong-gu, Suwon, 443-721, Republic of Korea. .,BK21 Plus Research Center for Biomedical Sciences, Ajou University Graduate School of Medicine, San 5 Woncheon-dong, Yeongtong-gu, Suwon, 443-721, Republic of Korea.
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8
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Mattei C, Lim R, Drury H, Nasr B, Li Z, Tadros MA, D'Abaco GM, Stok KS, Nayagam BA, Dottori M. Generation of Vestibular Tissue-Like Organoids From Human Pluripotent Stem Cells Using the Rotary Cell Culture System. Front Cell Dev Biol 2019; 7:25. [PMID: 30891447 PMCID: PMC6413170 DOI: 10.3389/fcell.2019.00025] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/12/2019] [Indexed: 01/17/2023] Open
Abstract
Hair cells are specialized mechanosensitive cells responsible for mediating balance and hearing within the inner ear. In mammals, hair cells are limited in number and do not regenerate. Human pluripotent stem cells (hPSCs) provide a valuable source for deriving human hair cells to study their development and design therapies to treat and/or prevent their degeneration. In this study we used a dynamic 3D Rotary Cell Culture System (RCCS) for deriving inner ear organoids from hPSCs. We show RCCS-derived organoids recapitulate stages of inner ear development and give rise to an enriched population of hair cells displaying vestibular-like morphological and physiological phenotypes, which resemble developing human fetal inner ear hair cells as well as the presence of accessory otoconia-like structures. These results show that hPSC-derived organoids can generate complex inner ear structural features and be a resource to study inner ear development.
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Affiliation(s)
- Cristiana Mattei
- Centre for Neural Engineering, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia.,Department of Biomedical Engineering, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Rebecca Lim
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia
| | - Hannah Drury
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia
| | - Babak Nasr
- Centre for Neural Engineering, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia.,Department of Electrical and Electronic Engineering, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia.,ARC Centre of Excellence for Integrative Brain Function, The University of Melbourne, Melbourne, VIC, Australia
| | - Zihui Li
- Department of Biomedical Engineering, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Melissa A Tadros
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia
| | - Giovanna M D'Abaco
- Department of Biomedical Engineering, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn S Stok
- Department of Biomedical Engineering, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Bryony A Nayagam
- Departments of Audiology and Speech Pathology and Department of Medical Bionics, The University of Melbourne, Melbourne, VIC, Australia
| | - Mirella Dottori
- Centre for Neural Engineering, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia.,Department of Biomedical Engineering, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
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9
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Darville LNF, Sokolowski BHA. Label-free quantitative mass spectrometry analysis of differential protein expression in the developing cochlear sensory epithelium. Proteome Sci 2018; 16:15. [PMID: 30127667 PMCID: PMC6091194 DOI: 10.1186/s12953-018-0144-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/26/2018] [Indexed: 12/27/2022] Open
Abstract
Background The sensory epithelium of the inner ear converts the mechanical energy of sound to electro-chemical energy recognized by the central nervous system. This process is mediated by receptor cells known as hair cells that express proteins in a timely fashion with the onset of hearing. Methods The proteomes of 3, 14, and 30 day-old mice cochlear sensory epithelia were revealed, using label-free quantitative mass spectrometry (LTQ-Orbitrap). Statistical analysis using a one-way ANOVA followed by Bonferroni’s post-hoc test was used to show significant differences in protein expression. Ingenuity Pathway Analysis was used to observe networks of differentially expressed proteins, their biological processes, and associated diseases, while Cytoscape software was used to determine putative interactions with select biomarker proteins. These candidate biomarkers were further verified using Western blotting, while coimmunoprecipitation was used to verify putative partners determined using bioinformatics. Results We show that a comparison across all three proteomes shows that there are 447 differentially expressed proteins, with 387 differentially expressed between postnatal day 3 and 30. Ingenuity Pathway Analysis revealed ~ 62% of postnatal day 3 downregulated proteins are involved in neurological diseases. Several proteins are expressed exclusively on P3, including Parvin α, Drebrin1 (Drb1), Secreted protein acidic and cysteine rich (SPARC), Transmembrane emp24 domain-containing protein 10 (Tmed10). Coimmunoprecipitations showed that Parvin and SPARC interact with integrin-linked protein kinase and the large conductance calcium-activated potassium channel, respectively. Conclusions Quantitative mass spectrometry revealed the identification of numerous differentially regulated proteins over three days of postnatal development. These data provide insights into functional pathways regulating normal sensory and supporting cell development in the cochlea that include potential biomarkers. Interacting partners of two of these markers suggest the importance of these complexes in regulating cellular structure and synapse development. Electronic supplementary material The online version of this article (10.1186/s12953-018-0144-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lancia N F Darville
- Morsani College of Medicine, Department of Otolaryngology-HNS, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612 USA
| | - Bernd H A Sokolowski
- Morsani College of Medicine, Department of Otolaryngology-HNS, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612 USA
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10
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Mass spectrometry quantitation of proteins from small pools of developing auditory and vestibular cells. Sci Data 2018; 5:180128. [PMID: 30015805 PMCID: PMC6049031 DOI: 10.1038/sdata.2018.128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/20/2018] [Indexed: 01/15/2023] Open
Abstract
Hair cells of the inner ear undergo postnatal development that leads to formation of their sensory organelles, synaptic machinery, and in the case of cochlear outer hair cells, their electromotile mechanism. To examine how the proteome changes over development from postnatal days 0 through 7, we isolated pools of 5000 Pou4f3-Gfp positive or negative cells from the cochlea or utricles; these cell pools were analysed by data-dependent and data-independent acquisition (DDA and DIA) mass spectrometry. DDA data were used to generate spectral libraries, which enabled identification and accurate quantitation of specific proteins using the DIA datasets. DIA measurements were extremely sensitive; we were able to detect proteins present at less than one part in 100,000 from only 312 hair cells. The DDA and DIA datasets will be valuable for accurately quantifying proteins in hair cells and non-hair cells over this developmental window.
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11
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Powles-Glover N, Maconochie M. Prenatal and postnatal development of the mammalian ear. Birth Defects Res 2017; 110:228-245. [DOI: 10.1002/bdr2.1167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/16/2017] [Accepted: 10/28/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Nicola Powles-Glover
- AstraZeneca, Innovative Medicines and Early Development; Drug Safety and Metabolism; Hertfordshire SG8 6HB United Kingdom
| | - Mark Maconochie
- Queen Mary University of London; London E1 4NS United Kingdom
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12
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Meese S, Cepeda AP, Gahlen F, Adams CM, Ficner R, Ricci AJ, Heller S, Reisinger E, Herget M. Activity-Dependent Phosphorylation by CaMKIIδ Alters the Ca 2+ Affinity of the Multi-C 2-Domain Protein Otoferlin. Front Synaptic Neurosci 2017; 9:13. [PMID: 29046633 PMCID: PMC5632675 DOI: 10.3389/fnsyn.2017.00013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/11/2017] [Indexed: 01/20/2023] Open
Abstract
Otoferlin is essential for fast Ca2+-triggered transmitter release from auditory inner hair cells (IHCs), playing key roles in synaptic vesicle release, replenishment and retrieval. Dysfunction of otoferlin results in profound prelingual deafness. Despite its crucial role in cochlear synaptic processes, mechanisms regulating otoferlin activity have not been studied to date. Here, we identified Ca2+/calmodulin-dependent serine/threonine kinase II delta (CaMKIIδ) as an otoferlin binding partner by pull-downs from chicken utricles and reassured interaction by a co-immunoprecipitation with heterologously expressed proteins in HEK cells. We confirmed the expression of CaMKIIδ in rodent IHCs by immunohistochemistry and real-time PCR. A proximity ligation assay indicates close proximity of the two proteins in rat IHCs, suggesting that otoferlin and CaMKIIδ also interact in mammalian IHCs. In vitro phosphorylation of otoferlin by CaMKIIδ revealed ten phosphorylation sites, five of which are located within C2-domains. Exchange of serines/threonines at phosphorylated sites into phosphomimetic aspartates reduces the Ca2+ affinity of the recombinant C2F domain 10-fold, and increases the Ca2+ affinity of the C2C domain. Concordantly, we show that phosphorylation of otoferlin and/or its interaction partners are enhanced upon hair cell depolarization and blocked by pharmacological CaMKII inhibition. We therefore propose that otoferlin activity is regulated by CaMKIIδ in IHCs.
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Affiliation(s)
- Sandra Meese
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, and Collaborative Research Center 889, University of Göttingen, Göttingen, Germany.,Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, Göttingen, Germany
| | - Andreia P Cepeda
- Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, Göttingen, Germany.,Molecular Biology of Cochlear Neurotransmission Group, Department of Otorhinolaryngology, University Medical Center Göttingen, and Collaborative Research Center 889, University of Göttingen, Göttingen, Germany
| | - Felix Gahlen
- Department of Otorhinolaryngology, Head and Neck Surgery, Ruhr-University Bochum, Bochum, Germany
| | - Christopher M Adams
- Stanford University Mass Spectrometry, Stanford University, Stanford, CA, United States
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, and Collaborative Research Center 889, University of Göttingen, Göttingen, Germany
| | - Anthony J Ricci
- Department of Otolaryngology, Head and Neck Surgery, Stanford School of Medicine, Stanford, CA, United States
| | - Stefan Heller
- Department of Otolaryngology, Head and Neck Surgery, Stanford School of Medicine, Stanford, CA, United States
| | - Ellen Reisinger
- Molecular Biology of Cochlear Neurotransmission Group, Department of Otorhinolaryngology, University Medical Center Göttingen, and Collaborative Research Center 889, University of Göttingen, Göttingen, Germany
| | - Meike Herget
- Department of Otolaryngology, Head and Neck Surgery, Stanford School of Medicine, Stanford, CA, United States
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13
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Global Analysis of Protein Expression of Inner Ear Hair Cells. J Neurosci 2016; 37:1320-1339. [PMID: 28039372 DOI: 10.1523/jneurosci.2267-16.2016] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 11/29/2016] [Accepted: 12/19/2016] [Indexed: 11/21/2022] Open
Abstract
The mammalian inner ear (IE) subserves auditory and vestibular sensations via highly specialized cells and proteins. Sensory receptor hair cells (HCs) are necessary for transducing mechanical inputs and stimulating sensory neurons by using a host of known and as yet unknown protein machinery. To understand the protein composition of these unique postmitotic cells, in which irreversible protein degradation or damage can lead to impaired hearing and balance, we analyzed IE samples by tandem mass spectrometry to generate an unbiased, shotgun-proteomics view of protein identities and abundances. By using Pou4f3/eGFP-transgenic mice in which HCs express GFP driven by Pou4f3, we FACS purified a population of HCs to analyze and compare the HC proteome with other IE subproteomes from sensory epithelia and whole IE. We show that the mammalian HC proteome comprises hundreds of uniquely or highly expressed proteins. Our global proteomic analysis of purified HCs extends the existing HC transcriptome, revealing previously undetected gene products and isoform-specific protein expression. Comparison of our proteomic data with mouse and human databases of genetic auditory/vestibular impairments confirms the critical role of the HC proteome for normal IE function, providing a cell-specific pool of candidates for novel, important HC genes. Several proteins identified exclusively in HCs by proteomics and verified by immunohistochemistry map to human genetic deafness loci, potentially representing new deafness genes. SIGNIFICANCE STATEMENT Hearing and balance rely on specialized sensory hair cells (HCs) in the inner ear (IE) to convey information about sound, acceleration, and orientation to the brain. Genetically and environmentally induced perturbations to HC proteins can result in deafness and severe imbalance. We used transgenic mice with GFP-expressing HCs, coupled with FACS sorting and tandem mass spectrometry, to define the most complete HC and IE proteome to date. We show that hundreds of proteins are uniquely identified or enriched in HCs, extending previous gene expression analyses to reveal novel HC proteins and isoforms. Importantly, deafness-linked proteins were significantly enriched in HCs, suggesting that this in-depth proteomic analysis of IE sensory cells may hold potential for deafness gene discovery.
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14
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Profiling Specific Inner Ear Cell Types Using Cell Sorting Techniques. Methods Mol Biol 2016. [PMID: 27259940 DOI: 10.1007/978-1-4939-3615-1_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Studies of specific tissue cell types are becoming increasingly important in advancing our understanding of cell biology and gene and protein expression. Prospective isolation of specific cell types is a powerful technique as it facilitates such investigations, allowing for analysis and characterization of individual cell populations. Such an approach to studying inner ear tissues presents a unique challenge because of the paucity of cells of interest and limited cell markers. In this chapter, we describe methods for selectively labeling and isolating different inner ear cell types from the neonatal mouse cochlea using fluorescence-activated cell sorting.
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15
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Alawieh A, Mondello S, Kobeissy F, Shibbani K, Bassim M. Proteomics studies in inner ear disorders: pathophysiology and biomarkers. Expert Rev Proteomics 2015; 12:185-96. [PMID: 25795149 DOI: 10.1586/14789450.2015.1024228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although proteomics has been exploited in a wide range of diseases for identification of biomarkers and pathophysiological mechanisms, there are still biomedical disciplines such as otology where proteomics platforms are underused due to technical challenges and/or complex features of the disease. Thus, in the past few years, healthcare and scientific agencies have advocated the development and adoption of proteomic technologies in otological research. However, few studies have been conducted and limited literature is available in this area. Here, we present the state of the art of proteomics in otology, discussing the substantial evidence from recent experimental models and clinical studies in inner-ear conditions. We also delineate a series of critical issues including minute size of the inner ear, delicacy and poor accessibility of tissue that researchers face while undertaking otology proteomics research. Furthermore, we provide perspective to enhance the impact and lead to the clinical implementation of these proteomics-based strategies.
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Affiliation(s)
- Ali Alawieh
- Department of Neurosciences, Medical University of South Carolina, Charleston, SC 29425, USA
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16
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Liu Q, Chen J, Gao X, Ding J, Tang Z, Zhang C, Chen J, Li L, Chen P, Wang J. Identification of stage-specific markers during differentiation of hair cells from mouse inner ear stem cells or progenitor cells in vitro. Int J Biochem Cell Biol 2015; 60:99-111. [PMID: 25582750 DOI: 10.1016/j.biocel.2014.12.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 12/10/2014] [Accepted: 12/31/2014] [Indexed: 12/11/2022]
Abstract
The induction of inner ear hair cells from stem cells or progenitor cells in the inner ear proceeds through a committed inner ear sensory progenitor cell stage prior to hair cell differentiation. To increase the efficacy of inducing inner ear hair cell differentiation from the stem cells or progenitor cells, it is essential to identify comprehensive markers for the stem cells/progenitor cells from the inner ear, the committed inner ear sensory progenitor cells and the differentiating hair cells to optimize induction conditions. Here, we report that we efficiently isolated and expanded the stem cells or progenitor cells from postnatal mouse cochleae, and induced the generation of inner ear progenitor cells and subsequent differentiation of hair cells. We profiled the gene expression of the stem cells or progenitor cells, the inner ear progenitor cells, and hair cells using aRNA microarray analysis. The pathway and gene ontology (GO) analysis of differentially expressed genes was performed. Analysis of genes exclusively detected in one particular cellular population revealed 30, 38, and 31 genes specific for inner ear stem cells, inner ear progenitor cells, and hair cells, respectively. We further examined the expression of these genes in vivo and determined that Gdf10+Ccdc121, Tmprss9+Orm1, and Chrna9+Espnl are marker genes specific for inner ear stem cells, inner ear progenitor cells, and differentiating hair cells, respectively. The identification of these marker genes will likely help the effort to increase the efficacy of hair cell induction from the stem cells or progenitor cells.
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Affiliation(s)
- Quanwen Liu
- Institute of Cell and Development, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Jiarong Chen
- Institute of Cell and Development, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xiangli Gao
- Laboratory of Bone Marrow, The First Hospital, Zhejiang University, Hangzhou, Zhejiang 310006, PR China
| | - Jie Ding
- Institute of Cell and Development, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zihua Tang
- Institute of Cell and Development, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Cui Zhang
- Institute of Cell and Development, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Jianling Chen
- Institute of Cell and Development, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Liang Li
- Institute of Cell and Development, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Ping Chen
- Institute of Cell and Development, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China; Departments of Cell Biology and Otolaryngology, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Jinfu Wang
- Institute of Cell and Development, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China.
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17
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Durruthy-Durruthy R, Heller S. Applications for single cell trajectory analysis in inner ear development and regeneration. Cell Tissue Res 2014; 361:49-57. [PMID: 25532874 DOI: 10.1007/s00441-014-2079-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 11/20/2014] [Indexed: 01/06/2023]
Abstract
Single cell trajectory analysis is a computational approach that orders cells along a pseudotime axis. This temporal modeling approach allows the characterization of transitional processes such as lineage development, response to insult, and tissue regeneration. The concept can also be applied to resolve spatial organization of cells within the originating tissue. Known as temporal and spatial transcriptomics, respectively, these methods belong to the most powerful analytical techniques for quantitative gene expression data currently available. Here, we discuss three different approaches: principal component analysis, the 'Monocle' algorithm, and self-organizing maps. We use a previously published qRT-PCR dataset of single neuroblast cells isolated from the developing mouse inner ear to highlight the basic features of the three methods and their individual limitations, as well as the distinct advantages that make them useful for research on the inner ear. The complex developmental morphogenesis of the inner ear and its specific challenges such as the paucity of cells as well as important open questions such as sensory hair cell regeneration render this organ a prime target for single cell trajectory analysis strategies.
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Affiliation(s)
- Robert Durruthy-Durruthy
- Department of Otolaryngology - HNSs, Stanford University School of Medicine, Stanford, CA, 94305, USA
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18
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Lundberg YW, Xu Y, Thiessen KD, Kramer KL. Mechanisms of otoconia and otolith development. Dev Dyn 2014; 244:239-53. [PMID: 25255879 DOI: 10.1002/dvdy.24195] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Otoconia are bio-crystals that couple mechanic forces to the sensory hair cells in the utricle and saccule, a process essential for us to sense linear acceleration and gravity for the purpose of maintaining bodily balance. In fish, structurally similar bio-crystals called otoliths mediate both balance and hearing. Otoconia abnormalities are common and can cause vertigo and imbalance in humans. However, the molecular etiology of these illnesses is unknown, as investigators have only begun to identify genes important for otoconia formation in recent years. RESULTS To date, in-depth studies of selected mouse otoconial proteins have been performed, and about 75 zebrafish genes have been identified to be important for otolith development. CONCLUSIONS This review will summarize recent findings as well as compare otoconia and otolith development. It will provide an updated brief review of otoconial proteins along with an overview of the cells and cellular processes involved. While continued efforts are needed to thoroughly understand the molecular mechanisms underlying otoconia and otolith development, it is clear that the process involves a series of temporally and spatially specific events that are tightly coordinated by numerous proteins. Such knowledge will serve as the foundation to uncover the molecular causes of human otoconia-related disorders.
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Affiliation(s)
- Yunxia Wang Lundberg
- Vestibular Genetics Laboratory, Boys Town National Research Hospital, Omaha, Nebraska
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19
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Lundberg YW, Xu Y, Thiessen KD, Kramer KL. Mechanisms of otoconia and otolith development. Dev Dyn 2014. [PMID: 25255879 DOI: 10.1002/dvdy.24195(2014)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Otoconia are bio-crystals that couple mechanic forces to the sensory hair cells in the utricle and saccule, a process essential for us to sense linear acceleration and gravity for the purpose of maintaining bodily balance. In fish, structurally similar bio-crystals called otoliths mediate both balance and hearing. Otoconia abnormalities are common and can cause vertigo and imbalance in humans. However, the molecular etiology of these illnesses is unknown, as investigators have only begun to identify genes important for otoconia formation in recent years. RESULTS To date, in-depth studies of selected mouse otoconial proteins have been performed, and about 75 zebrafish genes have been identified to be important for otolith development. CONCLUSIONS This review will summarize recent findings as well as compare otoconia and otolith development. It will provide an updated brief review of otoconial proteins along with an overview of the cells and cellular processes involved. While continued efforts are needed to thoroughly understand the molecular mechanisms underlying otoconia and otolith development, it is clear that the process involves a series of temporally and spatially specific events that are tightly coordinated by numerous proteins. Such knowledge will serve as the foundation to uncover the molecular causes of human otoconia-related disorders.
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Affiliation(s)
- Yunxia Wang Lundberg
- Vestibular Genetics Laboratory, Boys Town National Research Hospital, Omaha, Nebraska
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20
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Abstract
Sensory hair cell loss is the major cause of hearing and balance disorders. Mammals are incapable of sustained hair cell regeneration, but lower vertebrates can regenerate these mechano-electrical transducers. We present the first comprehensive transcriptome (by mRNA-Seq) of hair cell regeneration in the chick utricle. We provide pathway and pattern annotations and correlate these with the phenotypic events that occur during regeneration. These patterns are surprisingly synchronous and highly punctuated. We show how these patterns are a new resource for identifying components of the hair cell transcriptome and identify 494 new putative hair-cell-specific genes and validate three of these (of three tested) by immunohistochemical staining. We describe many surprising new components and dynamic expression patterns, particularly within NOTCH signaling. For example, we show that HES7 is specifically expressed during utricle hair cell regeneration and closely parallels the expression of HES5. Likewise, the expression of ATOH1 is closely correlated with HEYL and the HLH inhibitory transcription factors ID1, ID2, and ID4. We investigate the correlation between fibroblast growth factor signaling and supporting cell proliferation and show that FGF20 inhibits supporting cell proliferation. We also present an analysis of 212 differentially expressed transcription factor genes in the regenerative time course that fall into nine distinct gene expression patterns, many of which correlate with phenotypic events during regeneration and represent attractive candidates for future analysis and manipulation of the regenerative program in sensory epithelia and other vertebrate neuroepithelia.
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